COX7A1
Basic information
Region (hg38): 19:36150922-36152449
Previous symbols: [ "COX7A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX7A1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in COX7A1
This is a list of pathogenic ClinVar variants found in the COX7A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-36150993-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 19-36151488-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 19-36151517-C-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 19-36151546-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 19-36151672-G-T | not specified | Uncertain significance (Jun 13, 2024) | ||
| 19-36151689-C-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 19-36151719-C-A | not specified | Uncertain significance (Oct 27, 2022) | ||
| 19-36152394-C-A | not specified | Uncertain significance (Feb 11, 2025) | ||
| 19-36152398-G-A | not specified | Uncertain significance (Dec 31, 2024) | ||
| 19-36152398-G-T | not specified | Uncertain significance (Jan 25, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COX7A1 | protein_coding | protein_coding | ENST00000292907 | 4 | 1948 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000373 | 0.223 | 125700 | 0 | 9 | 125709 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.549 | 39 | 49.9 | 0.781 | 0.00000330 | 496 |
| Missense in Polyphen | 14 | 19.383 | 0.72228 | 210 | ||
| Synonymous | 1.11 | 14 | 20.4 | 0.688 | 0.00000125 | 149 |
| Loss of Function | -0.532 | 6 | 4.75 | 1.26 | 2.55e-7 | 47 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000967 | 0.0000967 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000311 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000101 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.;
- Pathway
- Cardiac muscle contraction - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.756
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.125
- hipred
- N
- hipred_score
- 0.213
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0628
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cox7a1
- Phenotype
- cellular phenotype; muscle phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- regulation of oxidative phosphorylation;generation of precursor metabolites and energy;electron transport chain;mitochondrial respirasome assembly;proton transmembrane transport
- Cellular component
- mitochondrion;mitochondrial respirasome;integral component of membrane
- Molecular function
- cytochrome-c oxidase activity